ArticleDatabase : the journal of biological databases and curation2019
PubTerm: a web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- A systematic review and functionalFrontiers in neuroscience · 2025Pooled it
- A systematic review and functional bioinformatics analysis of genes associated with Crohn's disease identify more than 120 related genes.BMC genomics · 2022Pooled it
- Identification of Potential Meniere's Disease Targets in the Adult Stria Vascularis.Frontiers in neurology · 2021Pooled it
- GPDminer: a tool for extracting named entities and analyzing relations in biological literature.BMC bioinformatics · 2024Article
- Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature.Systematic reviews · 2023Article
- SIB Literature Services: RESTful customizable search engines in biomedical literature, enriched with automatically mapped biomedical concepts.Nucleic acids research · 2020Article
- PubTator central: automated concept annotation for biomedical full text articles.Nucleic acids research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Background and objective: Analysis, annotation and curation of biomedical scientific literature is a recurrent task in biomedical research, database curation and clinics. Commonly, the reading is centered on concepts such as genes, diseases or molecules. Database curators may also need to annotate published abstracts related to a specific topic. However, few free and intuitive tools exist to assist users in this context. Therefore, we developed PubTerm, a web tool to organize, categorize, curate and annotate a large number of PubMed abstracts related to biological entities such as genes, diseases, chemicals, species, sequence variants and other related information. Methods: A variety of interfaces were implemented to facilitate curation and annotation, including the organization of abstracts by terms, by the co-occurrence of terms or by specific phrases. Information includes statistics on the occurrence of terms. The abstracts, terms and other related information can be annotated and categorized using user-defined categories. The session information can be saved and restored, and the data can be exported to other formats. Results: The pipeline in PubTerm starts by specifying a PubMed query or list of PubMed identifiers. Then, the user can specify three lists of categories and specify what information will be highlighted in which colors. The user then utilizes the `term view' to organize the abstracts by gene, disease, species or other information to facilitate the annotation and categorization of terms or abstracts. Other views also facilitate the exploration of abstracts and connections between terms. We have used PubTerm to quickly and efficiently curate collections of more than 400 abstracts that mention more than 350 genes to generate revised lists of susceptibility genes for diseases. An example is provided for pulmonary arterial hypertension. Conclusions: PubTerm saves time for literature revision by assisting with annotation organization and knowledge acquisition.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.